Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. - Mi-Youn K. Brusniak; Bernd Bodenmiller; David S. Campbell; Kelly Cooke; James Eddes; Andrew Garbutt; Hollis Lau; Simon Letarte; Lukas N. Mueller; Vagisha Sharma; Olga Vitek; Ning Zhang; et al. (BMC Bioinform., 2008)

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. - Mi-Youn K. Brusniak; Sung-Tat Kwok; Mark Christiansen; David S. Campbell; Lukas Reiter; Paola Picotti; Ulrike Kusebauch; Hector Ramos; Eric W. Deutsch; Jingchun Chen; Robert L. Moritz; Ruedi Aebersold (BMC Bioinform., 2011)

Automated Mouse Organ Segmentation: A Deep Learning Based Solution. - Naveen Ashish; Mi-Youn K. Brusniak (BCB, 2018)

Laboratory information management software for engineered mini-protein therapeutic workflow. - Mi-Youn K. Brusniak; Hector Ramos; Bernard Lee; James M. Olson (BMC Bioinform., 2019)